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Research paper | Open Access

A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max

Anqi Zhanga,1, Tangchao Konga,1, Baiquan Sunb,1, Shizheng Qiua,1, Jiahe Guoa, Shuyong Ruana, Yu Guoa, Jirui Guoa, Zhishuai Zhanga, Yue Liua, Zheng Hua, Tao Jianga, Yadong Liua, Shuqi Caoa, Shi Sunb, Tingting Wub, Huilong Hongc, Bingjun Jiangb, Maoxiang Yangb, Xiangyu Yaob, Yang Hua(), Bo Liua(), Tianfu Hanb(), Yadong Wanga()
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

1 These authors contributed equally to this work.

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Abstract

Soybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar Zhonghuang 13 (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution.

Keywords

SoybeanTelomere-to-Telomere assemblyZhonghuang 13Structure variations

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The Crop Journal
Volume 12 Issue 1,
February 2024
Pages 142-153
DOI: 10.1016/j.cj.2023.10.003
Cite this article:
Zhang A, Kong T, Sun B, et al. A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max. The Crop Journal, 2024, 12(1): 142-153. https://doi.org/10.1016/j.cj.2023.10.003
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